---
_id: '20780'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analysed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find the
majority of turnovers happened in the group Schizophora, which tend to have fewer
genes on the F element (the chromosome homologous to the ancestral insect X chromosome)
than lower dipterans, a factor previously hypothesized to facilitate turnover.
Most derived X chromosomes have higher GC content than autosomes, consistent with
a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene
movement out of the X is detected for most of these new X chromosomes, and many
of these moved genes have high testis expression in Drosophila, suggesting that
out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences
of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20780
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20780.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria,
2025.
ista: Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome
turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780.
mla: Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome
Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).
corr_author: '1'
date_created: 2025-12-10T23:40:14Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-15T11:13:32Z
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-20780
file:
- access_level: open_access
checksum: 251e7aab01917c2ad2fbccf465492ea1
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:47:15Z
date_updated: 2025-12-11T10:47:15Z
file_id: '20799'
file_name: Perl_scripts.zip
file_size: 4575
relation: main_file
success: 1
- access_level: open_access
checksum: daf1c03149dd170b14e5c8e109ee3c77
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:52:17Z
date_updated: 2025-12-11T10:52:17Z
file_id: '20800'
file_name: Supplementary_Datasets.zip
file_size: 19052849
relation: main_file
success: 1
- access_level: open_access
checksum: 658d6e95a361b0a3db058b7b4e1733d4
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:52:11Z
date_updated: 2025-12-11T10:52:11Z
file_id: '20801'
file_name: Supplementary_Tables.zip
file_size: 566476
relation: main_file
success: 1
- access_level: open_access
checksum: 2a2b92eb9fade0015719190596a8c5b7
content_type: text/plain
creator: llayanaf
date_created: 2025-12-11T11:00:53Z
date_updated: 2025-12-11T11:00:53Z
file_id: '20802'
file_name: README.txt
file_size: 1204
relation: main_file
success: 1
file_date_updated: 2025-12-11T11:00:53Z
has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '12'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
status: public
title: Causes and consequences of sex-chromosome turnovers in Diptera
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20796'
abstract:
- lang: eng
text: Rapid prophase chromosome movements ensure faithful alignment of the parental
homologous chromosomes and successful synapsis formation during meiosis. These
movements are driven by cytoplasmic forces transmitted to the nuclear periphery,
where chromosome ends are attached through transmembrane proteins. During many
developmental stages a specific genome architecture with chromatin nuclear periphery
contacts mediates specific gene expression. Whether chromatin is removed from
the nuclear periphery as a consequence of chromosome motions or by a specific
mechanism is not fully understood. Here, we identify a mechanism to remove chromatin
from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation
of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early
prophase of meiosis. Interfering with chromatin removal delays chromosome pairing,
impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis.
Long read sequencing reveals deletions and duplications in offspring lacking VRK-1
underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability
in gametes during rapid chromosome movements.
acknowledgement: We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi
Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for
sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics
facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and
Nick Wedige) for training and support in image acquisition. We also thank the members
of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian
Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B
(ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory
for helpful discussions. Some strains were provided by the Caenorhabditis Genetics
Center, which is funded by the National Institutes of Health Office of Research
Infrastructure Programs (P40OD010440).
article_number: '10446'
article_processing_charge: Yes
article_type: original
author:
- first_name: Dimitra
full_name: Paouneskou, Dimitra
last_name: Paouneskou
- first_name: Antoine
full_name: Baudrimont, Antoine
last_name: Baudrimont
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Angela
full_name: Graf, Angela
last_name: Graf
- first_name: Shehab
full_name: Moukbel Ali Aldawla, Shehab
last_name: Moukbel Ali Aldawla
- first_name: Claudia
full_name: Kölbl, Claudia
last_name: Kölbl
- first_name: Irene
full_name: Tiemann-Boege, Irene
last_name: Tiemann-Boege
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Verena
full_name: Jantsch, Verena
last_name: Jantsch
citation:
ama: Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 2025;16. doi:10.1038/s41467-025-65420-9
apa: Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel
Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic
chromosomes from the nuclear periphery is important for genome integrity. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65420-9
chicago: Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi,
Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz
Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65420-9.
ieee: D. Paouneskou et al., “BAF-1–VRK-1 mediated release of meiotic chromosomes
from the nuclear periphery is important for genome integrity,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla
S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 16, 10446.
mla: Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications,
vol. 16, 10446, Springer Nature, 2025, doi:10.1038/s41467-025-65420-9.
short: D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel
Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications
16 (2025).
date_created: 2025-12-11T10:45:06Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2025-12-15T09:28:37Z
day: '25'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1038/s41467-025-65420-9
external_id:
pmid:
- '41290579'
file:
- access_level: open_access
checksum: a952f7ea050242b79008540de49a0e61
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T09:25:51Z
date_updated: 2025-12-15T09:25:51Z
file_id: '20823'
file_name: 2025_NatureComm_Paouneskou.pdf
file_size: 8096309
relation: main_file
success: 1
file_date_updated: 2025-12-15T09:25:51Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery
is important for genome integrity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20797'
abstract:
- lang: eng
text: Quantum key distribution (QKD) offers a theoretically secure method to share
secret keys, yet practical implementations face challenges due to noise and loss
over long-distance channels. Traditional QKD protocols require extensive noise
compensation, hindering their industrial scalability and lowering the achievable
key rates. Alternative protocols encode logical qubits in noise-resilient states
but at the cost of using many physical qubits, increasing susceptibility to loss
and limiting transmission distance. In this work, we introduce a logical-qubit
encoding that uses antisymmetric Bell states in the continuous photonic degrees
of freedom, frequency and time. By leveraging the continuous space, we overcome
this noise-loss robustness trade-off by minimizing the number of photons per logical
qubit while optimizing the encoding resilience over noise fluctuations. We analyze
the security of our encoding and demonstrate its robustness compared to existing
state-of-the-art protocols. This approach provides a path toward scalable, efficient
QKD implementations under realistic noise conditions.
acknowledgement: We thank B. Baragiola, A. Boubriak, M. Clark, M. Jones, and P. Skrzypczyk
for useful discussions. H.S. acknowledges financial support from EPSRC Quantum Engineering
Centre for Doctoral Training Grant No. EP/SO23607/1. E.L. acknowledges support from
the Engineering and Physical Sciences Research Council (EPSRC) Hub in Quantum Computing
and Simulation (EP/T001062/1). T.S. acknowledges that they received no funding in
support of this research. M.P.S. acknowledges support from the EPSRC Quantum Engineering
Centre for Doctoral Training EP/SO23607/1 and the European Commission through Starting
Grant No. ERC-2018-STG803665 (PEQEM). G.R. acknowledges support from the Royal Commission
for the Exhibition of 1851 through a Research Fellowship, from the European Commission
through Starting Grant No. ERC-2018-STG803665 (PEQEM) and Advanced Grant No. ERC-2020-ADG101021085
(FLQuant), and from EPSRC through Standard Proposal Grant No. EP/X016218/1 (Mono-Squeeze).
article_number: '024072'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Hannah
full_name: Seabrook, Hannah
last_name: Seabrook
- first_name: Emilien
full_name: Lavie, Emilien
last_name: Lavie
- first_name: Karl T
full_name: Strömberg, Karl T
id: 68011cd2-da32-11ee-a930-b2774c7aba5f
last_name: Strömberg
- first_name: Matthew P.
full_name: Stafford, Matthew P.
last_name: Stafford
- first_name: Giulia
full_name: Rubino, Giulia
last_name: Rubino
citation:
ama: Seabrook H, Lavie E, Strömberg KT, Stafford MP, Rubino G. Surpassing the loss-noise
robustness trade-off in quantum key distribution. Physical Review Applied.
2025;24(2). doi:10.1103/xq2l-r4r7
apa: Seabrook, H., Lavie, E., Strömberg, K. T., Stafford, M. P., & Rubino, G.
(2025). Surpassing the loss-noise robustness trade-off in quantum key distribution.
Physical Review Applied. American Physical Society. https://doi.org/10.1103/xq2l-r4r7
chicago: Seabrook, Hannah, Emilien Lavie, Karl T Strömberg, Matthew P. Stafford,
and Giulia Rubino. “Surpassing the Loss-Noise Robustness Trade-off in Quantum
Key Distribution.” Physical Review Applied. American Physical Society,
2025. https://doi.org/10.1103/xq2l-r4r7.
ieee: H. Seabrook, E. Lavie, K. T. Strömberg, M. P. Stafford, and G. Rubino, “Surpassing
the loss-noise robustness trade-off in quantum key distribution,” Physical
Review Applied, vol. 24, no. 2. American Physical Society, 2025.
ista: Seabrook H, Lavie E, Strömberg KT, Stafford MP, Rubino G. 2025. Surpassing
the loss-noise robustness trade-off in quantum key distribution. Physical Review
Applied. 24(2), 024072.
mla: Seabrook, Hannah, et al. “Surpassing the Loss-Noise Robustness Trade-off in
Quantum Key Distribution.” Physical Review Applied, vol. 24, no. 2, 024072,
American Physical Society, 2025, doi:10.1103/xq2l-r4r7.
short: H. Seabrook, E. Lavie, K.T. Strömberg, M.P. Stafford, G. Rubino, Physical
Review Applied 24 (2025).
date_created: 2025-12-11T10:46:28Z
date_published: 2025-08-29T00:00:00Z
date_updated: 2025-12-15T09:40:58Z
day: '29'
ddc:
- '530'
department:
- _id: OnHo
doi: 10.1103/xq2l-r4r7
external_id:
arxiv:
- '2412.08694'
file:
- access_level: open_access
checksum: 12ddb0414780f65b8e690fe0e6cfb95e
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T09:39:12Z
date_updated: 2025-12-15T09:39:12Z
file_id: '20824'
file_name: 2025_PhysReviewApplied_Seabrook.pdf
file_size: 3028735
relation: main_file
success: 1
file_date_updated: 2025-12-15T09:39:12Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Surpassing the loss-noise robustness trade-off in quantum key distribution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2025'
...
---
_id: '20804'
abstract:
- lang: eng
text: RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters
the nucleus, where it transcribes protein-coding genes. Although transcription
by Pol II is intensively studied, how this central multi-subunit enzyme is made
and the role of dedicated factors remains unclear. Here, we report the integrative
structural analysis of a native human Pol II from the cytoplasm captured near
the end of biogenesis. The complex contained Gdown1 and three biogenesis factors
– RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the
complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature
association of transcription factors. Further biochemical and cryo-EM analysis
revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of
the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results
uncover a network of interactions that chaperone cytoplasmic Pol II to prevent
aberrant interactions, reveal a GTP-controlled switch during the final stages
of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop
GTPase family of enzymes.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank A. Salmazo for assistance with Pol II purification. We thank
staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry
analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research
was further supported by the Scientific Service Units (SSUs) of IST Austria through
resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF),
Scientific Computing (SciComp), and the Preclinical Facility (PCF).
article_processing_charge: No
author:
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Benjamin
full_name: Neuditschko, Benjamin
last_name: Neuditschko
- first_name: Ulla
full_name: Schellhaas, Ulla
last_name: Schellhaas
- first_name: Clemens
full_name: Plaschka, Clemens
last_name: Plaschka
- first_name: Franz
full_name: Herzog, Franz
last_name: Herzog
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure
of cytoplasmic RNA polymerase II. 2025. doi:10.64898/2025.12.10.692585
apa: Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &
Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. bioRxiv. https://doi.org/10.64898/2025.12.10.692585
chicago: Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka,
Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.”
bioRxiv, 2025. https://doi.org/10.64898/2025.12.10.692585.
ieee: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C.
Bernecky, “Structure of cytoplasmic RNA polymerase II.” bioRxiv, 2025.
ista: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C.
2025. Structure of cytoplasmic RNA polymerase II. 10.64898/2025.12.10.692585.
mla: Hlavata, Annamaria, et al. Structure of Cytoplasmic RNA Polymerase II.
bioRxiv, 2025, doi:10.64898/2025.12.10.692585.
short: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky,
(2025).
corr_author: '1'
date_created: 2025-12-11T13:33:27Z
date_published: 2025-12-10T00:00:00Z
date_updated: 2025-12-15T09:48:22Z
day: '10'
department:
- _id: CaBe
doi: 10.64898/2025.12.10.692585
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.64898/2025.12.10.692585
month: '12'
oa: 1
oa_version: None
publication_status: published
publisher: bioRxiv
status: public
title: Structure of cytoplasmic RNA polymerase II
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20814'
abstract:
- lang: eng
text: We characterize all semigroups sandwiched between the semigroup of a Dirichlet
form and the semigroup of its active main part. In case the Dirichlet form is
regular, we give a more explicit description of the quadratic forms of the sandwiched
semigroups in terms of pairs consisting of an open set and a measure on an abstract
boundary.
acknowledgement: "Open Access funding enabled and organized by Projekt DEAL. The first
three authors acknowledge financial support of the DFG within the priority programme
Geometry at Infinity.\r\nM.W. acknowledges financial support by the German Academic
Scholarship Foundation, by the Austrian Science Fund (FWF) through grant number
F65 and the Esprit Programme [ESP 156], and by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation programme (grant
agreement No 716117)."
article_number: '6'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Matthias
full_name: Keller, Matthias
last_name: Keller
- first_name: Daniel
full_name: Lenz, Daniel
last_name: Lenz
- first_name: Marcel
full_name: Schmidt, Marcel
last_name: Schmidt
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Keller M, Lenz D, Schmidt M, Schwarz M, Wirth M. Boundary representations of
intermediate forms between a regular Dirichlet form and its active main part.
Potential Analysis. 2025;64. doi:10.1007/s11118-025-10251-y
apa: Keller, M., Lenz, D., Schmidt, M., Schwarz, M., & Wirth, M. (2025). Boundary
representations of intermediate forms between a regular Dirichlet form and its
active main part. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-025-10251-y
chicago: Keller, Matthias, Daniel Lenz, Marcel Schmidt, Michael Schwarz, and Melchior
Wirth. “Boundary Representations of Intermediate Forms between a Regular Dirichlet
Form and Its Active Main Part.” Potential Analysis. Springer Nature, 2025.
https://doi.org/10.1007/s11118-025-10251-y.
ieee: M. Keller, D. Lenz, M. Schmidt, M. Schwarz, and M. Wirth, “Boundary representations
of intermediate forms between a regular Dirichlet form and its active main part,”
Potential Analysis, vol. 64. Springer Nature, 2025.
ista: Keller M, Lenz D, Schmidt M, Schwarz M, Wirth M. 2025. Boundary representations
of intermediate forms between a regular Dirichlet form and its active main part.
Potential Analysis. 64, 6.
mla: Keller, Matthias, et al. “Boundary Representations of Intermediate Forms between
a Regular Dirichlet Form and Its Active Main Part.” Potential Analysis,
vol. 64, 6, Springer Nature, 2025, doi:10.1007/s11118-025-10251-y.
short: M. Keller, D. Lenz, M. Schmidt, M. Schwarz, M. Wirth, Potential Analysis
64 (2025).
date_created: 2025-12-14T23:02:03Z
date_published: 2025-12-03T00:00:00Z
date_updated: 2025-12-15T13:11:24Z
day: '03'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s11118-025-10251-y
ec_funded: 1
external_id:
arxiv:
- '2301.01035'
has_accepted_license: '1'
intvolume: ' 64'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s11118-025-10251-y
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833
grant_number: ESP156_N
name: Gradient flow techniques for quantum Markov semigroups
publication: Potential Analysis
publication_identifier:
eissn:
- 1572-929X
issn:
- 0926-2601
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary representations of intermediate forms between a regular Dirichlet
form and its active main part
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20816'
abstract:
- lang: eng
text: "Background: DNA methylation (DNAm) can regulate gene expression, and its
genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for
complex traits. The relative stability of methylation profiles may enable better
assessment of chronic exposures compared to single time-point protein measures.
We present the first large-scale epigenetic study of the highly-abundant serum
proteome measured via ultra-high throughput mass spectrometry in 14,671 samples
from the Generation Scotland cohort. We further demonstrate the first large-scale
comparison of protein EpiScores and their respective proteins as predictors of
incident cardiovascular disease.\r\n\r\nResults: Marginal epigenome-wide association
models, adjusting for age, sex, measurement batch, estimated white cell proportions,
BMI, smoking and methylation principal components, reveal 15,855 significant CpG
– protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10.
Bayesian epigenome-wide association studies of the same 133 proteins reveal 697
CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein
EpiScores correlate significantly with their respective protein in a holdout test-set.
Of these, sixteen associate significantly with incident all-cause cardiovascular
disease (Nevents=191) compared to one measured protein.\r\n\r\nConclusions: We
highlight a complex interplay between the blood-based methylome and proteome.
Importantly, we show that protein EpiScores correlate with measured proteins and
demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically
relevant biomarkers. The protein EpiScores demonstrate more significant associations
with cardiovascular disease than directly measured proteins, suggesting their
potential as clinical biomarkers for monitoring or predicting disease risk. We
suggest that biomarker development could be enhanced by the consideration of protein
EpiScores alongside measured proteins."
acknowledgement: "Generation Scotland received core support from the Chief Scientist
Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish
Funding Council [HR03006] and is currently supported by the Wellcome Trust [216767/Z/19/Z].
Genotyping of the Generation Scotland samples was carried out by the Genetics Core
Laboratory at the Edinburgh Clinical Research Facility, University of Edinburgh,
Scotland and was funded by the Medical Research Council UK and the Wellcome Trust
(Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally”
(STRADL) Reference 104036/Z/14/Z). The DNA methylation profiling and analysis was
supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI:
Prof AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard)
and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Prof
HC Whalley).\r\nJAR is a University of Edinburgh Clinical Academic Track PhD student,
supported by the Wellcome Trust (319878/Z/24/Z). ADC was supported by a Medical
Research Council PhD Studentship in Precision Medicine with funding from the Medical
Research Council Doctoral Training Program and the University of Edinburgh College
of Medicine and Veterinary Medicine. HMS is a student on the University of Edinburgh
Translational Neuroscience PhD programme funded by the Wellcome Trust (218493/Z/19/Z).
CH was funded by MRC Human Genetics Unit program (QTL in Health and Disease) (grant
U.MC_UU_00007/10). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (221890/Z/20/Z). JM and REM were supported
by Alzheimer’s Society project grant AS-PG-19b-010."
article_number: '417'
article_processing_charge: Yes
article_type: original
author:
- first_name: Josephine A.
full_name: Robertson, Josephine A.
last_name: Robertson
- first_name: Jakub
full_name: Bajzik, Jakub
id: b995e25b-8c4b-11ed-a6d8-f71b7bcd6122
last_name: Bajzik
- first_name: Spyros
full_name: Vernardis, Spyros
last_name: Vernardis
- first_name: Aleksandra D.
full_name: Chybowska, Aleksandra D.
last_name: Chybowska
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Arturas
full_name: Grauslys, Arturas
last_name: Grauslys
- first_name: Jure
full_name: Mur, Jure
last_name: Mur
- first_name: Hannah M.
full_name: Smith, Hannah M.
last_name: Smith
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Camilla
full_name: Drake, Camilla
last_name: Drake
- first_name: Hannah
full_name: Grant, Hannah
last_name: Grant
- first_name: Jamie
full_name: Pearce, Jamie
last_name: Pearce
- first_name: Tom C.
full_name: Russ, Tom C.
last_name: Russ
- first_name: Poppy
full_name: Adkin, Poppy
last_name: Adkin
- first_name: Matthew
full_name: White, Matthew
last_name: White
- first_name: Charles
full_name: Brigden, Charles
last_name: Brigden
- first_name: Christoph B.
full_name: Messner, Christoph B.
last_name: Messner
- first_name: David J.
full_name: Porteous, David J.
last_name: Porteous
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Aleksej
full_name: Zelezniak, Aleksej
last_name: Zelezniak
- first_name: Markus
full_name: Ralser, Markus
last_name: Ralser
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Robertson JA, Bajzik J, Vernardis S, et al. Methylome-wide association studies
and epigenetic biomarker development for 133 mass spectrometry-assessed circulating
proteins in 14,671 Generation Scotland participants. Genome Biology. 2025;26.
doi:10.1186/s13059-025-03892-0
apa: Robertson, J. A., Bajzik, J., Vernardis, S., Chybowska, A. D., Mccartney, D.
L., Grauslys, A., … Marioni, R. E. (2025). Methylome-wide association studies
and epigenetic biomarker development for 133 mass spectrometry-assessed circulating
proteins in 14,671 Generation Scotland participants. Genome Biology. Springer
Nature. https://doi.org/10.1186/s13059-025-03892-0
chicago: Robertson, Josephine A., Jakub Bajzik, Spyros Vernardis, Aleksandra D.
Chybowska, Daniel L. Mccartney, Arturas Grauslys, Jure Mur, et al. “Methylome-Wide
Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed
Circulating Proteins in 14,671 Generation Scotland Participants.” Genome Biology.
Springer Nature, 2025. https://doi.org/10.1186/s13059-025-03892-0.
ieee: J. A. Robertson et al., “Methylome-wide association studies and epigenetic
biomarker development for 133 mass spectrometry-assessed circulating proteins
in 14,671 Generation Scotland participants,” Genome Biology, vol. 26. Springer
Nature, 2025.
ista: Robertson JA, Bajzik J, Vernardis S, Chybowska AD, Mccartney DL, Grauslys
A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P,
White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser
M, Robinson MR, Marioni RE. 2025. Methylome-wide association studies and epigenetic
biomarker development for 133 mass spectrometry-assessed circulating proteins
in 14,671 Generation Scotland participants. Genome Biology. 26, 417.
mla: Robertson, Josephine A., et al. “Methylome-Wide Association Studies and Epigenetic
Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins
in 14,671 Generation Scotland Participants.” Genome Biology, vol. 26, 417,
Springer Nature, 2025, doi:10.1186/s13059-025-03892-0.
short: J.A. Robertson, J. Bajzik, S. Vernardis, A.D. Chybowska, D.L. Mccartney,
A. Grauslys, J. Mur, H.M. Smith, A. Campbell, C. Drake, H. Grant, J. Pearce, T.C.
Russ, P. Adkin, M. White, C. Brigden, C.B. Messner, D.J. Porteous, C. Hayward,
S.R. Cox, A. Zelezniak, M. Ralser, M.R. Robinson, R.E. Marioni, Genome Biology
26 (2025).
date_created: 2025-12-14T23:02:04Z
date_published: 2025-12-08T00:00:00Z
date_updated: 2025-12-15T13:19:41Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13059-025-03892-0
external_id:
pmid:
- '41361833'
file:
- access_level: open_access
checksum: 7c92919af1b5820d01e91e08906a411f
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T13:18:07Z
date_updated: 2025-12-15T13:18:07Z
file_id: '20825'
file_name: 2025_GenomeBiology_Robertson.pdf
file_size: 2206991
relation: main_file
success: 1
file_date_updated: 2025-12-15T13:18:07Z
has_accepted_license: '1'
intvolume: ' 26'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1474-760X
issn:
- 1474-7596
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Methylome-wide association studies and epigenetic biomarker development for
133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland
participants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '20817'
abstract:
- lang: eng
text: We present Mechanistic PDE Networks -- a model for discovery of governing
partial differential equations from data. Mechanistic PDE Networks represent spatiotemporal
data as space-time dependent linear partial differential equations in neural network
hidden representations. The represented PDEs are then solved and decoded for specific
tasks. The learned PDE representations naturally express the spatiotemporal dynamics
in data in neural network hidden space, enabling increased modeling power. Solving
the PDE representations in a compute and memory-efficient way, however, is a significant
challenge. We develop a native, GPU-capable, parallel, sparse and differentiable
multigrid solver specialized for linear partial differential equations that acts
as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose
a discovery architecture that can discovers nonlinear PDEs in complex settings,
while being robust to noise. We validate PDE discovery on a number of PDEs including
reaction-diffusion and Navier-Stokes equations.
acknowledgement: "AP. This project has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.\r\nFL. This research was funded in whole or in part
by the Austrian Science Fund (FWF) 10.55776/COE12. For open access purposes, the
author has applied a CC BY public\r\ncopyright license to any author accepted manuscript
version arising from this submission."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Adeel A
full_name: Pervez, Adeel A
id: fca6d90c-d47f-11ee-bc87-93ff51604981
last_name: Pervez
- first_name: Efstratios
full_name: Gavves, Efstratios
last_name: Gavves
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Pervez AA, Gavves E, Locatello F. Mechanistic PDE networks for discovery of
governing equations. In: 42nd International Conference on Machine Learning.
Vol 267. ML Research Press; 2025:48962-48973.'
apa: 'Pervez, A. A., Gavves, E., & Locatello, F. (2025). Mechanistic PDE networks
for discovery of governing equations. In 42nd International Conference on Machine
Learning (Vol. 267, pp. 48962–48973). Vancouver, Canada: ML Research Press.'
chicago: Pervez, Adeel A, Efstratios Gavves, and Francesco Locatello. “Mechanistic
PDE Networks for Discovery of Governing Equations.” In 42nd International Conference
on Machine Learning, 267:48962–73. ML Research Press, 2025.
ieee: A. A. Pervez, E. Gavves, and F. Locatello, “Mechanistic PDE networks for discovery
of governing equations,” in 42nd International Conference on Machine Learning,
Vancouver, Canada, 2025, vol. 267, pp. 48962–48973.
ista: 'Pervez AA, Gavves E, Locatello F. 2025. Mechanistic PDE networks for discovery
of governing equations. 42nd International Conference on Machine Learning. ICML:
International Conference on Machine Learning, PMLR, vol. 267, 48962–48973.'
mla: Pervez, Adeel A., et al. “Mechanistic PDE Networks for Discovery of Governing
Equations.” 42nd International Conference on Machine Learning, vol. 267,
ML Research Press, 2025, pp. 48962–73.
short: A.A. Pervez, E. Gavves, F. Locatello, in:, 42nd International Conference
on Machine Learning, ML Research Press, 2025, pp. 48962–48973.
conference:
end_date: 2025-07-19
location: Vancouver, Canada
name: 'ICML: International Conference on Machine Learning'
start_date: 2025-07-13
corr_author: '1'
date_created: 2025-12-14T23:02:04Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-12-16T12:24:55Z
day: '01'
ddc:
- '000'
department:
- _id: FrLo
ec_funded: 1
external_id:
arxiv:
- '2502.18377'
file:
- access_level: open_access
checksum: 933cb673fb41416f537278fb990df6c3
content_type: application/pdf
creator: dernst
date_created: 2025-12-16T12:21:49Z
date_updated: 2025-12-16T12:21:49Z
file_id: '20827'
file_name: 2025_ICML_Pervez.pdf
file_size: 993381
relation: main_file
success: 1
file_date_updated: 2025-12-16T12:21:49Z
has_accepted_license: '1'
intvolume: ' 267'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 48962-48973
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 42nd International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ alpz/mech-nn-discovery-pde
scopus_import: '1'
status: public
title: Mechanistic PDE networks for discovery of governing equations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 267
year: '2025'
...
---
OA_type: closed access
_id: '20818'
abstract:
- lang: eng
text: "This study demonstrates that Marchantia non-canonical PINs are predominantly
localized to the plasma membrane, with MpPINX and MpPINW exhibiting asymmetric
distribution.\r\nA newly identified miniW domain within the MpPINW hydrophilic
loop governs subcellular trafficking and asymmetric PM localization of non-canonical
PINs in Marchantia."
acknowledgement: The authors sincerely thank Dr. Shutang Tan for experimental support
and Dr. Barbara Kloeckener Gruissem for critical reading and constructive advice
on the manuscript. This study was supported by the European Research Council Advanced
Grant (ETAP-742985 to H.T. and J.F.), by the Ministry of Science and Technology
(grant 112-2636-B-005-001- to K.-J.L.), and by the Ministry of Education (grant
MOE-109-YSFAG-0006-001-P1 to K.-J.L.).
article_processing_charge: No
article_type: comment
author:
- first_name: Han
full_name: Tang, Han
id: 19BDF720-25A0-11EA-AC6E-928F3DDC885E
last_name: Tang
orcid: 0000-0001-6152-6637
- first_name: Adrijana
full_name: Smoljan, Adrijana
id: cced8a85-223e-11ed-af04-b0596c55053b
last_name: Smoljan
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Kuan Ju
full_name: Lu, Kuan Ju
last_name: Lu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. The miniW domain directs
polarized membrane localization of non-canonical PINs in Marchantia polymorpha.
Plant Cell and Environment. 2025. doi:10.1111/pce.70295
apa: Tang, H., Smoljan, A., Zou, M., Zhang, Y., Lu, K. J., & Friml, J. (2025).
The miniW domain directs polarized membrane localization of non-canonical PINs
in Marchantia polymorpha. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.70295
chicago: Tang, Han, Adrijana Smoljan, Minxia Zou, Yuzhou Zhang, Kuan Ju Lu, and
Jiří Friml. “The MiniW Domain Directs Polarized Membrane Localization of Non-Canonical
PINs in Marchantia Polymorpha.” Plant Cell and Environment. Wiley, 2025.
https://doi.org/10.1111/pce.70295.
ieee: H. Tang, A. Smoljan, M. Zou, Y. Zhang, K. J. Lu, and J. Friml, “The miniW
domain directs polarized membrane localization of non-canonical PINs in Marchantia
polymorpha,” Plant Cell and Environment. Wiley, 2025.
ista: Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. 2025. The miniW domain
directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha.
Plant Cell and Environment.
mla: Tang, Han, et al. “The MiniW Domain Directs Polarized Membrane Localization
of Non-Canonical PINs in Marchantia Polymorpha.” Plant Cell and Environment,
Wiley, 2025, doi:10.1111/pce.70295.
short: H. Tang, A. Smoljan, M. Zou, Y. Zhang, K.J. Lu, J. Friml, Plant Cell and
Environment (2025).
date_created: 2025-12-14T23:02:05Z
date_published: 2025-12-03T00:00:00Z
date_updated: 2025-12-15T13:56:26Z
day: '03'
department:
- _id: JiFr
doi: 10.1111/pce.70295
ec_funded: 1
external_id:
pmid:
- '41340422'
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Cell and Environment
publication_identifier:
eissn:
- 1365-3040
issn:
- 0140-7791
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The miniW domain directs polarized membrane localization of non-canonical PINs
in Marchantia polymorpha
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18753'
abstract:
- lang: eng
text: "We continue a line of research which studies which hereditary families of
digraphs have bounded dichromatic number. For a class of digraphs C, a hero in
\ C is any digraph H\r\n such that H -free digraphs in C have bounded dichromatic
number. We show that if F\r\n is an oriented star of degree at least five, the
only heroes for the class of F -free digraphs are transitive tournaments. For
oriented stars F of degree exactly four, we show the only heroes in F -free
digraphs are transitive tournaments, or possibly special joins of transitive tournaments.
Aboulker et al. characterized the set of heroes of {H,K1+P2→} -free digraphs
almost completely, and we show the same characterization for the class of {H,rK1+P3→}
-free digraphs. Lastly, we show that if we forbid two \"valid\" orientations of
brooms, then every transitive tournament is a hero for this class of digraphs."
acknowledgement: "We thank the anonymous referees for their careful proofreading which
helped improve the presentation of this paper. We also thank one of the anonymous
referees for pointing out our construction implies Theorem 1.7!\r\nBenjamin Moore
finished this project while a postdoctoral researcher at Charles University, and
was supported by project 22-17398S (Flows and cycles in graphs on surfaces) of the
Czech Science Foundation. Benjamin Moore is currently funded by RANDSTRUCT No. 101076777,
and appreciates the gracious support. We acknowledge the support of the Natural
Sciences and Engineering Research Council of Canada (NSERC), [funding reference
number RGPIN-2020-03912]. Cette recherche a été financée par le Conseil de recherches
en sciences naturelles et en génie du Canada (CRSNG), [numéro de référence RGPIN-2020-03912].
This project was funded in part by the Government of Ontario ."
article_number: '104104'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Alvaro
full_name: Carbonero, Alvaro
last_name: Carbonero
- first_name: Hidde
full_name: Koerts, Hidde
last_name: Koerts
- first_name: Benjamin
full_name: Moore, Benjamin
id: 6dc1a1be-bf1c-11ed-8d2b-d044840f49d6
last_name: Moore
- first_name: Sophie
full_name: Spirkl, Sophie
last_name: Spirkl
citation:
ama: Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden
induced forests. European Journal of Combinatorics. 2025;125. doi:10.1016/j.ejc.2024.104104
apa: Carbonero, A., Koerts, H., Moore, B., & Spirkl, S. (2025). On heroes in
digraphs with forbidden induced forests. European Journal of Combinatorics.
Elsevier. https://doi.org/10.1016/j.ejc.2024.104104
chicago: Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On
Heroes in Digraphs with Forbidden Induced Forests.” European Journal of Combinatorics.
Elsevier, 2025. https://doi.org/10.1016/j.ejc.2024.104104.
ieee: A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with
forbidden induced forests,” European Journal of Combinatorics, vol. 125.
Elsevier, 2025.
ista: Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with
forbidden induced forests. European Journal of Combinatorics. 125, 104104.
mla: Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.”
European Journal of Combinatorics, vol. 125, 104104, Elsevier, 2025, doi:10.1016/j.ejc.2024.104104.
short: A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics
125 (2025).
corr_author: '1'
date_created: 2025-01-05T23:01:55Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-05-19T14:06:00Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1016/j.ejc.2024.104104
external_id:
arxiv:
- '2306.04710'
isi:
- '001400113700001'
file:
- access_level: open_access
checksum: 2c75f78f40ebb93d16fe3765bda2905a
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:16:25Z
date_updated: 2025-04-16T09:16:25Z
file_id: '19577'
file_name: 2025_EuropJournCombinatorics_Carbonero.pdf
file_size: 1110657
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:16:25Z
has_accepted_license: '1'
intvolume: ' 125'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: European Journal of Combinatorics
publication_identifier:
issn:
- 0195-6698
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On heroes in digraphs with forbidden induced forests
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 125
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18754'
abstract:
- lang: eng
text: 'Exploring the molecular correlates of metabolic health measures may identify
their shared and unique biological processes and pathways. Molecular proxies of
these traits may also provide a more objective approach to their measurement.
Here, DNA methylation (DNAm) data were used in epigenome-wide association studies
(EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits:
body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures
of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000
volunteers from the Generation Scotland (GS) cohort. We observed a maximum of
12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression
EWAS. By contrast, a joint and conditional Bayesian penalized regression approach
yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed
well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936
[LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and
total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance
in the measured traits, respectively. The corresponding results in LBC1936 were
14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat,
where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups
but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function
in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05).
Accounting for the correlation structure across the methylome can vastly affect
the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly
applicable across populations and can reflect differences in cognition.'
article_processing_charge: No
article_type: original
author:
- first_name: Hannah M.
full_name: Smith, Hannah M.
last_name: Smith
- first_name: Hong Kiat
full_name: Ng, Hong Kiat
last_name: Ng
- first_name: Joanna E.
full_name: Moodie, Joanna E.
last_name: Moodie
- first_name: Danni A.
full_name: Gadd, Danni A.
last_name: Gadd
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Elena
full_name: Bernabeu, Elena
last_name: Bernabeu
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Paul
full_name: Redmond, Paul
last_name: Redmond
- first_name: Adele
full_name: Taylor, Adele
last_name: Taylor
- first_name: Danielle
full_name: Page, Danielle
last_name: Page
- first_name: Janie
full_name: Corley, Janie
last_name: Corley
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Darwin
full_name: Tay, Darwin
last_name: Tay
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: John C.
full_name: Chambers, John C.
last_name: Chambers
- first_name: Marie
full_name: Loh, Marie
last_name: Loh
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
citation:
ama: Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts. American Journal of Human Genetics.
2025;112(1):106-115. doi:10.1016/j.ajhg.2024.11.012
apa: Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu,
E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits
in Scottish and Singaporean cohorts. American Journal of Human Genetics.
Elsevier. https://doi.org/10.1016/j.ajhg.2024.11.012
chicago: Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel
L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors
of Metabolic Traits in Scottish and Singaporean Cohorts.” American Journal
of Human Genetics. Elsevier, 2025. https://doi.org/10.1016/j.ajhg.2024.11.012.
ieee: H. M. Smith et al., “DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts,” American Journal of Human Genetics,
vol. 112, no. 1. Elsevier, pp. 106–115, 2025.
ista: Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A,
Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson
MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based
predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal
of Human Genetics. 112(1), 106–115.
mla: Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits
in Scottish and Singaporean Cohorts.” American Journal of Human Genetics,
vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:10.1016/j.ajhg.2024.11.012.
short: H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu,
A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J.
Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni,
R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.
date_created: 2025-01-05T23:01:56Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-02-27T12:38:23Z
day: '02'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2024.11.012
external_id:
isi:
- '001412498600001'
pmid:
- '39706196'
file:
- access_level: open_access
checksum: 891d120554f07da2c35d38388c29a690
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T09:26:42Z
date_updated: 2025-01-08T09:26:42Z
file_id: '18776'
file_name: 2025_AJHG_Smith.pdf
file_size: 2266488
relation: main_file
success: 1
file_date_updated: 2025-01-08T09:26:42Z
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 106-115
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/marioni-group/Metabolic_trait
scopus_import: '1'
status: public
title: DNA methylation-based predictors of metabolic traits in Scottish and Singaporean
cohorts
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2025'
...
---
OA_type: closed access
_id: '18765'
abstract:
- lang: eng
text: Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach
coupling differential fluorescent labeling to genetic manipulations in dividing
cells and their lineages. MADM uniquely enables the generation and visualization
of individual control or homozygous mutant cells in a heterozygous genetic environment.
Among its diverse applications, MADM has been used to dissect cell-autonomous
gene functions important for cortical development and neural development in general.
The high cellular resolution offered by MADM also permits the analysis of transcriptomic
changes of individual cells upon genetic manipulations. In this chapter, we describe
an experimental protocol combining the generation and isolation of MADM-labeled
cells with downstream single-cell RNA-sequencing technologies to probe cell-type
specific phenotypes due to genetic mutations at single-cell resolution.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank all Hippenmeyer lab members for support and discussions.
Experimental steps described were optimized with support provided by the Imaging
& Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter
Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine
(CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship).
This work was supported by ISTA institutional funds: The Austrian Science Fund Special
Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant
Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).
In: Garcia-Marques J, Lee T, eds. Lineage Tracing. Vol 2886. MIMB. New
York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7'
apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage
Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7'
chicago: 'Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM).” In Lineage Tracing, edited by Jorge Garcia-Marques
and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.'
ieee: 'G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity
of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double
Markers (MADM),” in Lineage Tracing, vol. 2886, J. Garcia-Marques and T.
Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.'
ista: 'Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of
Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers
(MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.'
mla: Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype
at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage
Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer
Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7.
short: G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.),
Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.
corr_author: '1'
date_created: 2025-01-07T08:36:47Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-04-14T07:43:46Z
day: '03'
department:
- _id: SiHi
doi: 10.1007/978-1-0716-4310-5_7
ec_funded: 1
editor:
- first_name: Jorge
full_name: Garcia-Marques, Jorge
last_name: Garcia-Marques
- first_name: Tzumin
full_name: Lee, Tzumin
last_name: Lee
external_id:
pmid:
- '39745639'
intvolume: ' 2886'
language:
- iso: eng
month: '01'
oa_version: None
page: 139-151
place: New York, NY
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Lineage Tracing
publication_identifier:
eisbn:
- '9781071643105'
eissn:
- 1940-6029
isbn:
- '9781071643099'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using
Mosaic Analysis with Double Markers (MADM)
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2886
year: '2025'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '18778'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryogenic-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how distinct
domains of the general transcription factor TFIIF control repressive activity.
Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions
and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding
assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU
data collection. We thank D. Slade (Max Perutz Laboratories and Medical University
of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank
N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of
Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The
funders had no role in study design, data collection and analysis, decision to publish
or preparation of the manuscript. This research was further supported by the Scientific
Service Units of ISTA through resources provided by the Laboratory Support Facility,
Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian
transcriptional repression by noncoding RNA. Nature Structural & Molecular
Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7
apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025).
Mechanism of mammalian transcriptional repression by noncoding RNA. Nature
Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7
chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie
Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.”
Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7.
ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism
of mammalian transcriptional repression by noncoding RNA,” Nature Structural
& Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025.
ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of
mammalian transcriptional repression by noncoding RNA. Nature Structural &
Molecular Biology. 32, 607–612.
mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32,
Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7.
short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural
& Molecular Biology 32 (2025) 607–612.
corr_author: '1'
date_created: 2025-01-08T11:20:20Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-11-20T10:28:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41594-024-01448-7
external_id:
isi:
- '001390268000001'
pmid:
- '39762629'
file:
- access_level: open_access
checksum: 2919b30b271f395888e880076a680d73
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T08:17:27Z
date_updated: 2025-04-16T08:17:27Z
file_id: '19573'
file_name: 2025_NatureStrucMolBiol_Tluckova.pdf
file_size: 9306639
relation: main_file
success: 1
file_date_updated: 2025-04-16T08:17:27Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 607-612
pmid: 1
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14644'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18820'
abstract:
- lang: eng
text: 'Feature selection is essential in the analysis of molecular systems and many
other fields, but several uncertainties remain: What is the optimal number of
features for a simplified, interpretable model that retains essential information?
How should features with different units be aligned, and how should their relative
importance be weighted? Here, we introduce the Differentiable Information Imbalance
(DII), an automated method to rank information content between sets of features.
Using distances in a ground truth feature space, DII identifies a low-dimensional
subset of features that best preserves these relationships. Each feature is scaled
by a weight, which is optimized by minimizing the DII through gradient descent.
This allows simultaneously performing unit alignment and relative importance scaling,
while preserving interpretability. DII can also produce sparse solutions and determine
the optimal size of the reduced feature space. We demonstrate the usefulness of
this approach on two benchmark molecular problems: (1) identifying collective
variables that describe conformations of a biomolecule, and (2) selecting features
for training a machine-learning force field. These results show the potential
of DII in addressing feature selection challenges and optimizing dimensionality
in various applications. The method is available in the Python library DADApy.'
acknowledgement: The authors thank Dr. Matteo Carli for providing the CLN025 replica
exchange MD trajectory and Matteo Allione for the fruitful discussions connected
with the idea of the linear scaling estimator. This work was partially funded by
NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum
Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial
support by the region Friuli Venezia Giulia (project F53C22001770002 received by
A.L.).
article_number: '270'
article_processing_charge: Yes
article_type: original
author:
- first_name: Romina
full_name: Wild, Romina
last_name: Wild
- first_name: Felix
full_name: Wodaczek, Felix
id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e
last_name: Wodaczek
orcid: 0009-0000-1457-795X
- first_name: Vittorio
full_name: Del Tatto, Vittorio
last_name: Del Tatto
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alessandro
full_name: Laio, Alessandro
last_name: Laio
citation:
ama: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection
and weighting in molecular systems using Differentiable Information Imbalance.
Nature Communications. 2025;16. doi:10.1038/s41467-024-55449-7
apa: Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., & Laio, A. (2025). Automatic
feature selection and weighting in molecular systems using Differentiable Information
Imbalance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55449-7
chicago: Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro
Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable
Information Imbalance.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55449-7.
ieee: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature
selection and weighting in molecular systems using Differentiable Information
Imbalance,” Nature Communications, vol. 16. Springer Nature, 2025.
ista: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature
selection and weighting in molecular systems using Differentiable Information
Imbalance. Nature Communications. 16, 270.
mla: Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular
Systems Using Differentiable Information Imbalance.” Nature Communications,
vol. 16, 270, Springer Nature, 2025, doi:10.1038/s41467-024-55449-7.
short: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications
16 (2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-02-27T12:41:25Z
day: '02'
ddc:
- '570'
department:
- _id: AnSa
- _id: BiCh
doi: 10.1038/s41467-024-55449-7
external_id:
isi:
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pmid:
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file:
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checksum: b3d0f3568d9a87c494cf231a5324029a
content_type: application/pdf
creator: dernst
date_created: 2025-01-14T06:59:25Z
date_updated: 2025-01-14T06:59:25Z
file_id: '18846'
file_name: 2025_NatureComm_Wild.pdf
file_size: 1216738
relation: main_file
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file_date_updated: 2025-01-14T06:59:25Z
has_accepted_license: '1'
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isi: 1
language:
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month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Automatic feature selection and weighting in molecular systems using Differentiable
Information Imbalance
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18821'
abstract:
- lang: eng
text: 'Even though the one-dimensional contact interaction requires no regularization,
renormalization methods have been shown to improve the convergence of numerical
calculations considerably. In this work, we compare and contrast these methods:
“the running coupling constant” where the two-body ground-state energy is used
as a renormalization condition, and two effective interaction approaches that
include information about the ground as well as excited states. In particular,
we calculate the energies and densities of few-fermion systems in a harmonic oscillator
with the configuration-interaction method and compare the results based upon renormalized
and bare interactions. We find that the use of the running coupling constant instead
of the bare interaction improves convergence significantly. A comparison with
an effective interaction, which is designed to reproduce the relative part of
the energy spectrum of two particles, showed a similar improvement. The effective
interaction provides an additional improvement if the center-of-mass excitations
are included in the construction. Finally, we discuss the transformation of observables
alongside the renormalization of the potential, and demonstrate that this might
be an essential ingredient for accurate numerical calculations.'
acknowledgement: We thank J. Cremon and J. Bjerlin for earlier contributions to the
configuration-interaction calculations used in this work (see Refs. [49,50]). F.B.
and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter,
and Lila Chergui. We further want to thank Lila Chergui for helpful comments on
the paper. This research was financially supported by the Knut and Alice Wallenberg
Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No.
2022-03654 VR).
article_number: '013303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Stephanie M.
full_name: Reimann, Stephanie M.
last_name: Reimann
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical
Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303
apa: Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison
of renormalized interactions using one-dimensional few-body systems as a testbed.
Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303
chicago: Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev.
“Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems
as a Testbed.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303.
ieee: F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of
renormalized interactions using one-dimensional few-body systems as a testbed,”
Physical Review A, vol. 111, no. 1. American Physical Society, 2025.
ista: Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical Review
A. 111(1), 013303.
mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional
Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303,
American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303.
short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111
(2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-02-27T12:41:58Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.111.013303
external_id:
arxiv:
- '2408.10052'
isi:
- '001398791400004'
intvolume: ' 111'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
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url: ' https://doi.org/10.48550/arXiv.2408.10052'
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison of renormalized interactions using one-dimensional few-body systems
as a testbed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18822'
abstract:
- lang: eng
text: Let N(X) be the number of integral zeros (mathematical equation). Works of
Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy
and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead
a natural large sieve inequality, we recover the same bound on N(X). This is part
of a more general statement, for diagonal cubic forms in (mathematical equation)
variables, where we allow approximations to Hasse–Weil L-functions.
acknowledgement: I thank Peter Sarnak for suggesting projects that ultimately led
to the present paper. I also thank him for many encouraging discussions, helpful
comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina
for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old
discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations
illuminating the combinatorics of an older, counting version of the present Lemma
4.9. Finally, special thanks are due to the editors and referees for their patience
and help with the exposition. This work was partially supported by NSF Grant DMS-1802211,
and the European Union's Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie Grant Agreement No. 101034413.
article_number: e70008
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Victor
full_name: Wang, Victor
id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9
last_name: Wang
orcid: 0000-0002-0704-7026
citation:
ama: Wang V. Diagonal cubic forms and the large sieve. Mathematika. 2025;71(1).
doi:10.1112/mtk.70008
apa: Wang, V. (2025). Diagonal cubic forms and the large sieve. Mathematika.
London Mathematical Society. https://doi.org/10.1112/mtk.70008
chicago: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika.
London Mathematical Society, 2025. https://doi.org/10.1112/mtk.70008.
ieee: V. Wang, “Diagonal cubic forms and the large sieve,” Mathematika, vol.
71, no. 1. London Mathematical Society, 2025.
ista: Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1),
e70008.
mla: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika,
vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:10.1112/mtk.70008.
short: V. Wang, Mathematika 71 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:01Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-04-14T07:54:56Z
day: '02'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1112/mtk.70008
ec_funded: 1
external_id:
isi:
- '001388255500001'
file:
- access_level: open_access
checksum: 700a8596b4bffce2320d074120962c22
content_type: application/pdf
creator: dernst
date_created: 2025-01-14T06:52:09Z
date_updated: 2025-01-14T06:52:09Z
file_id: '18845'
file_name: 2025_Mathematika_Wang.pdf
file_size: 309893
relation: main_file
success: 1
file_date_updated: 2025-01-14T06:52:09Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Mathematika
publication_identifier:
eissn:
- 2041-7942
issn:
- 0025-5793
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagonal cubic forms and the large sieve
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18823'
article_number: kiae651
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dechang
full_name: Cao, Dechang
last_name: Cao
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
citation:
ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651'
apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures:
DNA methylation alterations across generations. Plant Physiology. Oxford
University Press. https://doi.org/10.1093/plphys/kiae651'
chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology. Oxford
University Press, 2025. https://doi.org/10.1093/plphys/kiae651.'
ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation
alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford
University Press, 2025.'
ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 197(1), kiae651.'
mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology, vol.
197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.'
short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:02Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-15T08:18:19Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiae651
external_id:
isi:
- '001382979900001'
pmid:
- '39691053'
file:
- access_level: open_access
checksum: a9b2a12d7bc6174f27e28413e9c77a9c
content_type: application/pdf
creator: dernst
date_created: 2025-07-15T08:17:25Z
date_updated: 2025-07-15T08:17:25Z
file_id: '20023'
file_name: 2025_PlantPhysiology_Cao.pdf
file_size: 1214018
relation: main_file
success: 1
file_date_updated: 2025-07-15T08:17:25Z
has_accepted_license: '1'
intvolume: ' 197'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory of maternal temperatures: DNA methylation alterations across generations'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2025'
...
---
_id: '18837'
abstract:
- lang: eng
text: Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
citation:
ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution
expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837
apa: Danzl, J. G., & Kreuzinger, C. (2025). Research Data for the publication
“Super-resolution expansion microscopy in plant roots.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:18837
chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication
‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837.
ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots.’” Institute of Science and Technology Austria,
2025.
ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:18837.
mla: Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication
“Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science
and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837.
short: J.G. Danzl, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
first_name: Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- contributor_type: researcher
first_name: Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- contributor_type: researcher
first_name: Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- contributor_type: researcher
first_name: Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
- contributor_type: researcher
first_name: Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- contributor_type: researcher
first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- contributor_type: researcher
first_name: Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- contributor_type: researcher
first_name: Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- contributor_type: researcher
first_name: Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
- contributor_type: researcher
first_name: Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- contributor_type: researcher
first_name: Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- contributor_type: researcher
first_name: Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- contributor_type: researcher
first_name: Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- contributor_type: researcher
first_name: Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- contributor_type: researcher
first_name: Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2025-01-13T09:51:29Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-10-08T08:43:55Z
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:18837
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status: public
title: Research Data for the publication "Super-resolution expansion microscopy in
plant roots"
tmp:
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...
---
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abstract:
- lang: eng
text: Type II CRISPR endonucleases are widely used programmable genome editing tools.
Recently, CRISPR-Cas systems with highly compact nucleases have been discovered,
including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures
of a Cas9d nuclease (747 amino acids in length) in multiple functional states,
revealing a stepwise process of DNA targeting involving a conformational switch
in a REC2 domain insertion. Our structures provide insights into the intricately
folded guide RNA which acts as a structural scaffold to anchor small, flexible
protein domains for DNA recognition. The sgRNA can be truncated by up to ~25%
yet still retain activity in vivo. Using ancestral sequence reconstruction, we
generated compact nucleases capable of efficient genome editing in mammalian cells.
Collectively, our results provide mechanistic insights into the evolution and
DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for
future re-engineering of minimal RNA-guided DNA endonucleases.
acknowledgement: We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for
assistance with the figures. We thank M. Hooper for assistance developing the GFP
assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz
and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory
at UT Austin. This work was funded, in part, by a sponsored research agreement with
Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T),
and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research
Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious
Diseases (NIAID 1R01AI110577 to K.A.J.).
article_number: '457'
article_processing_charge: Yes
article_type: original
author:
- first_name: Rodrigo Fregoso
full_name: Ocampo, Rodrigo Fregoso
last_name: Ocampo
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Isabel
full_name: Nocedal, Isabel
last_name: Nocedal
- first_name: Samatar A.
full_name: Jirde, Samatar A.
last_name: Jirde
- first_name: Lisa M.
full_name: Alexander, Lisa M.
last_name: Alexander
- first_name: Nicole C.
full_name: Thomas, Nicole C.
last_name: Thomas
- first_name: Anjali
full_name: Das, Anjali
last_name: Das
- first_name: Sarah
full_name: Nielson, Sarah
last_name: Nielson
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: Christopher T.
full_name: Brown, Christopher T.
last_name: Brown
- first_name: Cristina N.
full_name: Butterfield, Cristina N.
last_name: Butterfield
- first_name: Daniela S.A.
full_name: Goltsman, Daniela S.A.
last_name: Goltsman
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d
and its resurrected ancestor. Nature Communications. 2025;16. doi:10.1038/s41467-024-55573-4
apa: Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S.
A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and
its resurrected ancestor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55573-4
chicago: Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield,
Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al.
“DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55573-4.
ieee: R. F. Ocampo et al., “DNA targeting by compact Cas9d and its resurrected
ancestor,” Nature Communications, vol. 16. Springer Nature, 2025.
ista: Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas
NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor
DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature
Communications. 16, 457.
mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected
Ancestor.” Nature Communications, vol. 16, 457, Springer Nature, 2025,
doi:10.1038/s41467-024-55573-4.
short: R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M.
Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield,
D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-07-03T11:58:22Z
day: '07'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-55573-4
external_id:
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publication: Nature Communications
publication_identifier:
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publisher: Springer Nature
quality_controlled: '1'
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title: DNA targeting by compact Cas9d and its resurrected ancestor
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18849'
abstract:
- lang: eng
text: Many biological systems operate near the physical limits to their performance,
suggesting that aspects of their behavior and underlying mechanisms could be derived
from optimization principles. However, such principles have often been applied
only in simplified models. Here, we explore a detailed mechanistic model of the
gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize
the information that gene expression levels provide about nuclear positions. This
optimization is conducted under realistic constraints, such as limits on the number
of available molecules. Remarkably, the optimal networks we derive closely match
the architecture and spatial gene expression profiles observed in the real organism.
Our framework quantifies the tradeoffs involved in maximizing functional performance
and allows for the exploration of alternative network configurations, addressing
the question of which features are necessary and which are contingent. Our results
suggest that multiple solutions to the optimization problem might exist across
closely related organisms, offering insights into the evolution of gene regulatory
networks.
acknowledgement: We thank Nicholas H. Barton for his comments on the manuscript, Benjamin
Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early
collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many
persistently inspiring conversations. This work was supported in part by the Human
Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European
Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for
the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730,
and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE
priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored
by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).
article_number: e2402925121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy
of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121
apa: Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving
a genetic regulatory network from an optimization principle. Proceedings of
the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121
chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik.
“Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121.
ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic
regulatory network from an optimization principle,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy of
Sciences. 122(1), e2402925121.
mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an
Optimization Principle.” Proceedings of the National Academy of Sciences,
vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121.
short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National
Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:26:51Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2402925121
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oa_version: Published Version
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project:
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call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
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grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
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grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
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title: Deriving a genetic regulatory network from an optimization principle
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volume: 122
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...
---
APC_amount: 2750 USD
OA_place: publisher
OA_type: hybrid
_id: '18850'
abstract:
- lang: eng
text: 'Biophysical constraints limit the specificity with which transcription factors
(TFs) can target regulatory DNA. While individual nontarget binding events may
be low affinity, the sheer number of such interactions could present a challenge
for gene regulation by degrading its precision or possibly leading to an erroneous
induction state. Chromatin can prevent nontarget binding by rendering DNA physically
inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by
pioneer factors (PFs). Under what conditions and by how much can chromatin reduce
regulatory errors on a global scale? We use a theoretical approach to compare
two scenarios for gene regulation: one that relies on TF binding to free DNA alone
and one that uses a combination of TFs and chromatin-regulating PFs to achieve
desired gene expression patterns. We find, first, that chromatin effectively silences
groups of genes that should be simultaneously OFF, thereby allowing more accurate
graded control of expression for the remaining ON genes. Second, chromatin buffers
the deleterious consequences of nontarget binding as the number of OFF genes grows,
permitting a substantial expansion in regulatory complexity. Third, chromatin-based
regulation productively co-opts nontarget TF binding for ON genes in order to
establish a “leaky” baseline expression level, which targeted activator or repressor
binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin
simultaneously alleviates pressure for high specificity of regulatory interactions
and enables an increase in genome size with minimal impact on global expression
error.'
acknowledgement: M.L.P. was supported by the European Molecular Biology Laboratory
(EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie
Skłodowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported
by EMBL Core Funding and Theory@EMBL. This work is supported by European Research
Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of
the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély,
for helpful feedback and discussion. We also thank EMBL IT Services for the use
of high performance computing resources.
article_number: e2411887121
article_processing_charge: No
article_type: original
author:
- first_name: Mindy Liu
full_name: Perkins, Mindy Liu
last_name: Perkins
- first_name: Justin
full_name: Crocker, Justin
last_name: Crocker
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene
regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2411887121
apa: Perkins, M. L., Crocker, J., & Tkačik, G. (2025). Chromatin enables precise
and scalable gene regulation with factors of limited specificity. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2411887121
chicago: Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables
Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2411887121.
ieee: M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable
gene regulation with factors of limited specificity,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable
gene regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 122(1), e2411887121.
mla: Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation
with Factors of Limited Specificity.” Proceedings of the National Academy of
Sciences, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025,
doi:10.1073/pnas.2411887121.
short: M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy
of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:27:25Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2411887121
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date_updated: 2025-01-20T09:38:32Z
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oa: 1
oa_version: Published Version
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project:
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grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
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publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
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url: https://github.com/officerredshirt/network_crosstalk
scopus_import: '1'
status: public
title: Chromatin enables precise and scalable gene regulation with factors of limited
specificity
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short: CC BY-NC-ND (4.0)
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volume: 122
year: '2025'
...